III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

A. UniVerse Alive: An Organic, Self-Made, Encoded, Familial Procreativity

Garcia-Ruiz, Juan Manuel, et al. Mineral Self-Organization on a Lifeless Planet. Physics of Life Reviews. January, 2020. JM G-R, University of Granada, Laboratory for the Study of Crystallogenesis, Mark van Zuilen, University of Paris, Institute of Earth Physics, and Wolfgang Bach, University of Bremen, each a veteran geoscientist, post a decisive report to date that Earth’s primordial land and sea materiality has an intrinsic propensity to catalyze, vivify, and develop into a prebiotic chemical milieu. As the 2010 decade of intensely accelerating worldwide research comes to a fruitful close like this, it is becoming possible to quantify and affirm that an organic universal genesis, an oriented evolutionary gestation to our curious, learned humankinder, does indeed exist on its independent own. See also for example, Inorganic Reactions Self-organize Life-like Microstructures Far from Equilibrium Knoll, Pamela and Oliver Steinbock by Pamela Knoll and Oliver Steinbock in the Israel Journal of Chemistry (58/6, 2018).

It has been experimentally found that, under alkaline conditions, silica is able to induce the formation of self-assembled inorganic-inorganic composite materials similar in morphology, texture and nanostructure to hybrid biomineral structures that, millions of years later, life was able to self-organize. These mineral self-organized structures (MISOS) have been shown to be effective catalyzers for prebiotic chemical reactions and to create compartmentalization within the solutions where they form. We reason that, during the very earliest history of this planet, there was a geochemical scenario that inevitably led to the existence of a large array of simple and complex organic compounds, many of which were relevant to prebiotic chemistry.

The primal phase involves a silica-rich high-pH ocean and is powered by two main factors: a) a quasi-infinite source of carbon molecules synthesized abiotically from serpentinization reaction, and b) the formation of self-organized silica-metal mineral composites that catalyze the condensation of molecules in a methane-rich reduced atmosphere. We discuss the plausibility of this geochemical scenario, review the details of the formation of MISOS and its catalytic properties and the transition towards a slightly alkaline to neutral ocean. (Abstract)

Gardner, James. A New Dawn for Cosmology. What is Enlightenment?. June-August, 2006. Noted more in Current Vistas, the author of Biocosm updates his case that much of cosmological physics is misconceived because the universe is fundamentally organic in kind.

Gardner, James. Biocosm. Makawao, HI: Inner Ocean Publishing, 2003. A spectulative attempt to gather and express the dawning vision in science of an organic cosmic genesis. By this view, a inherently self-organizing universe results in intelligent, planetary entities who can intentionally continue this complex development onto solar, galactic and cosmic scales. The author provides a synthesis of many thinkers in this regard such as Lee Smolin, Stuart Kauffman, Christian de Duve, Martin Rees and Lynn Margulis. From these sources is described a teleological evolution whose life and cognition is involved with the ultimate ‘self-replication’ of the universe. A bit heavy on technology but one of the early signs of an epic shift to a life-friendly cosmos.

Goodwin, Jay, et al. Digital and Analog Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. Goodwin, Anil Mehta and David Lynn (search), Emory University, NSF/NASA Center for Chemical Evolution researchers, highlight these dual reciprocal modes, as the quotes explain, as bytes and waves of interactivity. At the outset, the authors ask whether such lively, pervasive emergence could indeed be realized as an innate, complementary propensity of a spontaneous materiality. Some pages on, it closes via the second quote, that into the 21st century, this seems in fact to be intentionally so, at once affirming Darwin’s intuition, and Lawrence Henderson’s 1913 prescience of a cosmic and earthly environment inherently fit for biological growth (American Naturalist 47/2). And worth noting, with such sanction its human co-creators may commence to “reinvent” and embellish a new sustainable earth.

Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. (Abstract excerpt)

A functional approach that looks beyond the phylogenetic event horizon of ribosome emergence may allow us to fundamentally reinvent chemical evolution, and address an issue that dates back at least to Charles Darwin’s suggestion of the warm pond where living matter first emerged. His speculation implied that evolution was an inherent property of matter and that by deciphering the chemical thresholds and physical limitations necessary for the emergence of molecular order, we can unlock and deconvolute the most elaborate, elegant, and complex hierarchical forms of matter through chemical evolution. (2197)

Gordon, Richard and Alexei Sharov, eds. Habitability of the Universe before Earth. Amsterdam: Academic Press/Elsevier, 2017. The veteran theoretical biologist editorial team (search each) gather a unique collection in the later 2010s which professes a natural cosmic conduciveness for organic chemicals to form and complexify on the way to life’s cellular evolutionary development on a special bioplanet. The main parts are Physical and Chemical Constraints, Predicting Habitability, Life in the Cosmic Scale, and System Properties of Life. Altogether the work is a grand affirmation to date of a true procreative universe. Choice chapters are Life before its Origin on Earth by Julian Chela-Flores, The Emergence of Structured, Living, and Conscious Matter in the Evolution of the Universe by Dorian Aur and Jack Tuszynski, Earth before Life by Caren Marzban, et al, Cosmic Evolution of Biochemistry by Aditya Chopra and Charles Lineweaver, and The Habitability of Our Evolving Galaxy by Michael Gowanlock and Ian Morrison.

Habitability of the Universe before Earth examines the times and places on Earth that might have provided suitable environments for life to occur. The universe changed considerably during the vast epoch between the Big Bang 13.8 billion years ago and the first evidence of life on Earth 4.3 billion years ago, providing significant time and space to contemplate where, when and under what circumstances life might have arisen. No other book covers this cosmic time period from the point of view of its potential for life. It covers a broad range of laboratory and field research into the origins and evolution of life on Earth, life in extreme environments and the search for habitable environments in our solar system and beyond, including exoplanets, exomoons and astronomical biosignatures.

Griffith, Elizabeth, et al. Ocean-Atmosphere Interactions in the Emergence of Complexity in Simple Chemical Systems. Accounts of Chemical Research. 45/12, 2012. Biophysicists Griffith, with Veronica Vaida, University of Colorado, and Adrian Tuck, Imperial College, London, quantify an astute observation that this aqueous-air interface, by way of aerosol vesicular sprays, is an ideal incubator for biomolecules and cells to complexify and evolve. As the quotes aver, it is notable that this work assumes an intrinsic milieu of nonequilibrium energies which serve to generate life’s nested scales of self-similar networks. In regard, as the condensed matter realm of statistical physics lately becomes pregnant with quickening life and mind, it portends a grand revolutionary genesis cosmos.

The prebiotic conversion of simple organic molecules into complex biopolymers necessary for life can only have emerged on a stage set by geophysics. The transition between “prebiotic soup,” the diverse mixture of small molecules, and complex, self-replicating organisms requires passing through the bottleneck of fundamental chemistry. In this Account, we examine how water–air interfaces, namely, the surfaces of lakes, oceans, and atmospheric aerosols on ancient Earth, facilitated the emergence of complex structures necessary for life. In addition, we provide a statistical mechanical approach to natural selection and emergence of complexity that proposes a link between these molecular mechanisms and macroscopic scales. Very large aerosol populations were ubiquitous on ancient Earth, and the surfaces of lakes, oceans, and atmospheric aerosols would have provided an auspicious environment for the emergence of complex structures necessary for life. The fluctuating exposure of the large, recycling aerosol populations to radiation, pressure, temperature, and humidity over geological time allows complexity to emerge from simple molecular precursors. We propose an approach that connects chemical statistical thermodynamics and the macroscopic world of the planetary ocean and atmosphere. (Abstract excerpts)

We note a formal equivalence involving scale invariance variables q and K9q) on one hand with statistical thermodynamic quantities temperature T, partition function f, and Gibbs free energy G on the other. This links the scale invariance and power law distributions observed. In monomer sequences in proteins and nucleic acids and their distributions with lipids in membranes. The folding of proteins and their binding to lipid rafts in micelles has also been observed to be fractal. (2111) It remains true that nonequilibrium statistical mechanics is a very difficult discipline without a rigorous mathematical foundation, a daunting prospect for a system as complex as the prebiotic Earth’s fluid envelope. However, it can be seen how these principles result in natural selection as an inherent property of a molecular population in a fluctuating medium occupying a space characterized by anisotropic boundary conditions. (2111)

Gruebele, Martin and Devarajan (Dave) Thirumalai. Perspectives: Reaches of Chemical Physics in Biology. Journal of Chemical Physics. 139/12, 2013. In this second decade of the 2ist century, senior University of Illinois and University of Maryland biophysicists introduce a special section on the Chemical Physics of Biological Systems as material cosmos and developmental life become once more an integral genesis. As an example, it is inferred that the self-assembly of proteins can be newly explained by way of statistical mechanics, which fulfills Ervin Schrodinger’s 1940’s prescience. While a “Biological Physics” is broached, work remains to sort out and clear up with a consistent, natural literacy and indeed philosophy, e.g., the phrase “molecular machinery” is still bandied. A typical paper herein is “Combinatoric Analysis of Heterogeneous Stochastic Self-Assembly” by Maria D’Orsogna, et al.

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry. (Abstract)

The collection of articles in this special issue shows that, in the current golden era of quantitative approaches to biological problems, the techniques of chemical physics already play a central role. It is not surprising that chemical physics should be vital to study biology, which differs from physics and chemistry in two unique aspects, namely, evolution and replication (information transfer from one generation to another). Both of these aspects involve chemical reactions carried out by the molecules of life (DNA, proteins, RNA) in a seemingly organized but noisy environment. Therefore, applications of chemical reaction rate theories, effects of molecular fluctuations in chemical reactions, statistical mechanics principles of self-assembly, and information transfer on mesoscopic scales are needed in describing cellular processes. (121701-1-2)

Gusev, Victor and Dirk Schulze-Makuch. Genetic Code: Lucky Chance or Fundamental Law of Nature? Physics of Life Reviews. 1/3, 2004. Rather than a “frozen accident,” the prebiotic rise of life and DNA is seen to be written into a universe that is much more biological in kind as previously thought. See also Perlovsky in Part II, The Spiral of Science, for a note about this new journal.

It becomes clear that the information code is intrinsically related to the physical laws of the universe, and thus life may be an inevitable outcome of our universe. The lack of success in explaining the origin of the code and life itself in the last several decades suggest that we miss something very fundamental about life, possible something fundamental about matter and the universe itself. (Abstract)

Harms, Michael and Joseph Thornton. Evolutionary Biochemistry: Revealing the Historical and Physical Causes of Protein Properties. Nature Reviews Genetics. 14/8, 2013. Among the thousands of scientific papers each month, this entry by a University of Oregon, biophysicist, and a University of Chicago, geneticist, is worth especial notice for its proposal of a salutary 21st century reunion of a past divide, as the quotes say, between a ground materiality and developing life. Just now, as many entries here attest, this parting and fracture from the 1950s, and earlier 1700s, between physical cosmology and biological emergence, is finally coming together again into the single, indivisible universe it truly is and must be. In respect, a cosmic Copernican revolution could be seen as underway in our collaborative midst. The authors do not go that far, but intimate a resolve to the conflict of vicarious selection alone and an obviously necessary generative source. But while evolving organisms manifest an internal vital activity, such basic “physical properties” are not yet seen as endowed with their own agency. The work remains to scope out, name, and sufficiently explain this genesis universe where earth and peoples are meant to be. Maybe the missing crucial element is something like a similar natural genetic code.

The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry. Explanations of these two kinds of causality — the purviews of evolutionary biology and biochemistry, respectively — are typically pursued in isolation, but many fundamental questions fall squarely at the interface of fields. Here we articulate the paradigm of evolutionary biochemistry, which aims to dissect the physical mechanisms and evolutionary processes by which biological molecules diversified and to reveal how their physical architecture facilitates and constrains their evolution. We show how an integration of evolution with biochemistry moves us towards a more complete understanding of why biological molecules have the properties that they do. (Abstract)

This tension (between biochemistry and evolutionary biology) hardened into a cultural and institutional split as the fields competed for resources and legitimacy. The two groups defined themselves as asking incommensurable questions with different scientific aesthetics: biochemists and molecular biologists dissect the underlying mechanism by which model systems function, whereas evolutionary biologists analyse how the diversity of living forms in nature came to be. At most institutions, biology departments split into separate entities, creating a barrier to interactions between biochemists and evolutionists. (550)

Contingency, predictability and optimality The previous sections present a puzzle. Many proteins display strong patterns of parallel evolution, amassing the same mutations in response to selection given their physical constraints; protein evolution therefore seems to be predictable and deterministic. However, mutations that do not alter the function of the protein are often required to open evolutionary paths, suggesting that evolutionary trajectories are often contingent on chance events that are invisible to selection; protein evolution therefore seems to be unpredictable and unlikely to be repeated. How can these two perspectives be reconciled? A closer look reveals that these findings are compatible with each other. The set of mutational pathways available to a protein because of epistasis and constraints depends on its position in a neutral network in sequence space. These networks appear to be vast: some protein families contain sequences that have little discernable homology but maintain the same fold, and even the same function. Thus although proteins within neutral networks by definition have similar folds and functions, they may have different sequences, and the effects of mutations on them may be different. (567)

Hazen, Robert. Evolution of Minerals. Scientific American. March, 2010. At the same while that authors Sean M. Carroll, Chris Impey, and Marcelo Gleiser conclude the multiverse to be without plan or point, scientific peer geochemist Hazen advocates a true cosmic genesis of which human persons have a central creative purpose. In addition to this popular article, see also Geosphere and Atmosphere herein, and the February 2010 Elements: An International Magazine of Mineralogy, Geochemistry, and Petrology for more technical info on how living systems via effects such as an increasing oxygenation served to engender new and more complex mineral compounds. A good site to reach it is http://elements.geoscienceworld.org/current.dtl. And in the same issue, appears a notable essay article by Hazen and Niles Eldredge on “Themes and Variations in Complex Systems.”

Viewing minerals in an evolutionary context also elucidates a more general theme of evolving systems throughout the cosmos. Simple states evolve into increasingly complicated states in many contexts: the evolution of chemical elements in stars, mineral evolution in planets, the molecular evolution that leads to the origin of life, and the familiar biological evolution through Darwinian natural selection. (65)

Thus, we live in a universe primed for complexification: hydrogen atoms form stars, stars form the elements of the periodic table, those elements form planets, which in turn form minerals abundantly. Minerals catalyze the formation of biomolecules, which on Earth led to life. In this sweeping scenario, minerals represent but one inexorable step in the evolution of a cosmos that is learning to know itself. (65)

Genesis: The Scientific Quest for Life's Origins. http://scienceandreligion.hampshire.edu/videos.php. A presentation on November 3, 2011 by the Carnegie Institute of Washington and George Mason University mineral geologist at Hampshire College, Amherst, MA, in their Science and Religion lecture series. It is to be posted in full at the above website. The talk title is from Hazen’s 2005 book (search) which stands as a good synopsis of the organic revolution. By any lights today biological complexity spontaneously self-organizes and emerges from chemical matter, at every sequential stage, through dynamic interactions amongst many component agents. Hazen is lately involved with the Deep Carbon Observatory (Google) which is finding signs of “deep life” at high temperatures several miles into earth’s surface. His 2011 surmise further affirms a material reality naturally made to spawn and evolve life and people. “Life arises inevitably unto consciousness as the way a universe comes to know itself.” We quote the talk Abstract.

How did life arise? Is life’s origin a cosmic imperative manifest throughout the cosmos, or is life an improbable accident, restricted to a few planets (or only one)? Scientists seek experimental and theoretical frameworks to deduce the origin of life. In this context the concept of emergent systems provides a unifying approach. Natural systems with many interacting components, such as molecules, cells or organisms, often display complex behavior not associated with their individual components. The origin of life can be modeled as a sequence of emergent events – the synthesis of biomolecules, the selection and organization of those small molecules into functional macromolecules, the emergence of self-replicating molecular systems, and the initiation of molecular natural selection – which transformed the lifeless geochemical world of oceans, atmosphere and rocks into a living planet.

Hazen, Robert. Symphony in C: Carbon and the Evolution of (Almost) Everything. New York: Norton, 2019. The veteran geochemist director of the Deep Carbon Observatory at the Carnegie Institute, Washington and prolific, collegial author (search) writes a lyrical tribute to the most important element for the biochemical evolutionary occasion of creatures and peoples. He is also a member of a symphony orchestra as a trumpeter, so chose to arrange the work in four Earth, Air, Fire and Water movements about these prime ways carbon serves this purpose. He also led the discovery (RH 2008) of the vital role played by diverse mineral surfaces in life’s origin, whose compositions are seen evolve in tandem with biospheric and atmospheric systems (see VI. B. 1. Geosphere).

Hazen goes on here to consider a “second genesis” on myriad exoplanets, which would have a unique mineralogy but, akin to George McGhee 2019, would largely retrace and repeat the same oriented development. In so doing, he notes that Jacques Monod’s 1970 claim of chance accident over innate necessity is a false dichotomy (also McGhee 2016). While local contingency is rife, these relatively inanimate and animate materials evolve and emerge from origins, through many organisms, and unto ourselves as if along a guiding course. See also Carbon in Earth edited by R. Hazen, et al in the Reviews in Mineralogy and Geochemistry (Volume 75, 2013) for earlier views. As one peruses this luminous edition, a 21st century revolution to a truly organic ecosmos with life and persons written in becomes increasingly, profoundly evident.

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